Internal jugular vein thrombosis is rare. It is often secondary to prolonged central venous cannulation and associated with local or distant malignancy. The authors present a case of intra-operative thrombosis of the internal jugular vein which complicated subsequent microvascular anastomosis of a radial forearm free flap. The management of the intra-operatively thrombosed internal jugular vein and alternative anastamotic options for the free flap are discussed.